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Sometime in the beginning of The Matrix Online, a Cypherite redpill named Cryptos began making speeches about re-insertion into the Matrix. Being angered about Neo's sacrifice being for nothing, Kid, along with Shimada forms E Pluribus Neo ("From Many, Neo"), to combat the Cypherite threat.

E Pluribus Neo has two subcells: radical groups, seeking to disrupt and destroy the Matrix and the Machines, and the more moderate groups, using more peaceful methods towards freeing minds. Regardless of individual views held by members, EPN is by and large considered a terrorist organization, and is viewed as responsible for forced awakenings and the use of code bombs against the bluepill population (in some cases, are not code bombs, but Code Pulse Devices, which do not force the awakening of bluepills but send a data flux code that analyzes the stream of data and returns analysis to the device). However, EPN does not condone acts of terrorism towards the general population of bluepills in any way, and most of these actions are perpetrated by splinter and fringe factions.